PNPT1 RNA-Seq in HepG2

General Information


RBP	PNPT1
Cell_Line	HepG2
Method	shRNA
Exp_Name	PNPT1-BGHLV22-HepG2
ENCODE_series_ID	ENCSR317QGL
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR880DEH
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	PNPT1-BGHLV22-37
Rep2	PNPT1-BGHLV22-38
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	70.9
Rep2_qPCR	72.5
Rep1_WB	73.1
Rep2_WB	70.7
Antibody Cat#	A303-917A
Antibody Lot#	A303-917A
Antibody DCC ID	ENCAB230SUL
Status	Released
Project	ENCODE3
ID	525

Experiment Information (Status: Released)

	BGHLV22-37	BGHLV22-38
idx	465	466
TRCN#_or_BGC#	TRCN0000035905	TRCN0000035905
shRNA_or_gRNA_sequence	CGCCAGAGATTGTGAAATATA	CGCCAGAGATTGTGAAATATA
PAM
Name	PNPT1	PNPT1
Sample_ID	BGHLV22-37	BGHLV22-38
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	PNPT1	PNPT1
qPCR_result	70.9	72.5
Ave_qPCR	71.7
RT-qPCR_primer-F	TCCTACTGCCCTAGGATTAGAAGTT
RT-qPCR_primer-R	AAAGCCTCATTCTTCCATCG
protein_conc	7310	6961
WB_result	73.1	70.7
Ave_WB	71.9
WB_DONE_date	4/14/2015
MW	86kDa
IP	1	1
antibody_Cat#	A303-917A	A303-917A
Antibody DCC ID	ENCAB230SUL	ENCAB230SUL
submitted_to_DCC_date	5/6/2015
Rep1_TPM	13.5	0
Rep2_TPM	14	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2534	2535

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PNPT1	Product_ID: A303-917A Lot_ID: 1 Source: Bethyl Labs Target Name: PNPT1-human

Experiment Status

	BGHLV22-37	BGHLV22-38
Sample_ID	BGHLV22-37	BGHLV22-38
Sample Name	PNPT1-BGHLV22-37	PNPT1-BGHLV22-38
Sample Name	PNPT1-BGHLV22-37	PNPT1-BGHLV22-38
RBP	PNPT1	PNPT1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	800	801

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-37	BGHLV22-38
Sample #
Sample Name	PNPT1-BGHLV22-37	PNPT1-BGHLV22-38
Sample_Name_Alias	PNPT1-BGHLV22-37	PNPT1-BGHLV22-38
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/G8.png	DNA_Library_LV20-22-23/set2/H1.png
RIN	10.0	9.7
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G2.png	RNA_Library_LV22-23-25/set1/H2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-37	BGHLV22-38
RBP	PNPT1	PNPT1
Batch_ID	BGHLV22	BGHLV22
WB_result	73.100	70.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2486	2487

Sequencing Information

	BGHLV22-37	BGHLV22-38
Sample_ID	BGHLV22-37	BGHLV22-38
Sample Name	PNPT1-BGHLV22-37	PNPT1-BGHLV22-38
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	60,440,000	53,870,000
total_aligned_reads	55,770,546	49,055,118
unique_aligned_reads	52,432,594	46,145,470
percent_uniqueAligned	0.86751	0.85661
correlation_replicates	0.994834	0.994834
spikein_reads	321,004	294,342
percent_spikeins	0.00531	0.00546
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1108	1109

Data Submission Information

	BGHLV22-37	BGHLV22-37
ENCODE_alias	brenton-graveley:PNPT1-BGHLV22	brenton-graveley:PNPT1-BGHLV22-HepG2
ENCODE_accession	ENCSR880DEH	ENCSR317QGL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-37	BGHLV22-37
Sample Name	PNPT1-BGHLV22-37	PNPT1-BGHLV22-37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2932	6859

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
PNPT1-BGHLV22-37_ACTGAT_L001_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1108	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16298
PNPT1-BGHLV22-37_ACTGAT_L001_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1108	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16338
PNPT1-BGHLV22-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1108					GRCh38	V40	PNPT1-BGHLV22-37_ACTGAT_L001_R1_001.fastq.gz,PNPT1-BGHLV22-37_ACTGAT_L001_R2_001.fastq.gz		ENCORE2	16436
PNPT1-BGHLV22-37_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1108					GRCh38	V40	PNPT1-BGHLV22-37/Aligned.sortedByCoord.out.bam		ENCORE2	16476
PNPT1-BGHLV22-37_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1108					GRCh38	V40	PNPT1-BGHLV22-37/Aligned.sortedByCoord.out.bam		ENCORE2	16516
PNPT1-BGHLV22-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1108					GRCh38	V40	PNPT1-BGHLV22-37/Aligned.sortedByCoord.out.bam		ENCORE2	16556
PNPT1-BGHLV22-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1108					GRCh38	V40	PNPT1-BGHLV22-37/Aligned.sortedByCoord.out.bam		ENCORE2	16596
PNPT1-BGHLV22-37_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1108					GRCh38	V40	PNPT1-BGHLV22-37_ACTGAT_L001_R1_001.fastq.gz,PNPT1-BGHLV22-37_ACTGAT_L001_R2_001.fastq.gz		ENCORE2	16636
PNPT1-BGHLV22-38_ATTCCT_L002_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1109	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16299
PNPT1-BGHLV22-38_ATTCCT_L002_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1109	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16339
PNPT1-BGHLV22-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1109					GRCh38	V40	PNPT1-BGHLV22-38_ATTCCT_L002_R1_001.fastq.gz,PNPT1-BGHLV22-38_ATTCCT_L002_R2_001.fastq.gz		ENCORE2	16437
PNPT1-BGHLV22-38_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1109					GRCh38	V40	PNPT1-BGHLV22-38/Aligned.sortedByCoord.out.bam		ENCORE2	16477
PNPT1-BGHLV22-38_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1109					GRCh38	V40	PNPT1-BGHLV22-38/Aligned.sortedByCoord.out.bam		ENCORE2	16517
PNPT1-BGHLV22-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1109					GRCh38	V40	PNPT1-BGHLV22-38/Aligned.sortedByCoord.out.bam		ENCORE2	16557
PNPT1-BGHLV22-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1109					GRCh38	V40	PNPT1-BGHLV22-38/Aligned.sortedByCoord.out.bam		ENCORE2	16597
PNPT1-BGHLV22-38_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1109					GRCh38	V40	PNPT1-BGHLV22-38_ATTCCT_L002_R1_001.fastq.gz,PNPT1-BGHLV22-38_ATTCCT_L002_R2_001.fastq.gz		ENCORE2	16637